shiftReadsByFrame {ribosomeProfilingQC} | R Documentation

## Shift reads by reading frame

### Description

Shift reads P site position by reading frame. After shifting, all reading frame will be set as 0

### Usage

    shiftReadsByFrame(reads, txdb)

### Arguments

`reads` | Output of getPsiteCoordinates
`txdb` | A TxDb object.

### Value

Reads with reading frame information

### Examples

    library(Rsamtools)
    bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                               package="ribosomeProfilingQC")
    yieldSize <- 10000000
    bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
    pc <- getPsiteCoordinates(bamfile, bestpsite=11)
    pc.sub <- pc[pc$qwidth %in% c(29, 30)]
    library(GenomicFeatures)
    library(BSgenome.Drerio.UCSC.danRer10)
    txdb <- makeTxDbFromGFF(system.file("extdata",
              "Danio_rerio.GRCz10.91.chr1.gtf.gz",
              package="ribosomeProfilingQC"),
              organism = "Danio rerio",
              chrominfo = seqinfo(Drerio)["chr1"],
              taxonomyId = 7955)
    pc.sub <- shiftReadsByFrame(pc.sub, txdb)

[Package ribosomeProfilingQC version 0.99.9 Index]